Me and some friends are gonna run through the JA setting as a pen & paper campaign, possibly also with some miniature wargaming for major battles. I would like your input on all this! What game system(s) to use? How to translate merc stats? Any other suggestions? How would you do something like this? What possibilites would porting JA to the pen & paper format bring with it?

Personally I would like to add the RPG aspects of FO to JA2 to make it really good. You can play as the loner or the squad and have full progression of characters through the game. Remove or raise level Cap and add in special abilities

Yeah, JA the computer game is not all that much of an RPG. But think of the possibilities you could have with a good dungeon master (I think that's the term).

Here are some of my ideas:

Becoming evil and defecting to Queen Deidranna's side
Hacking into Deidranna's computer network (Gumpy!) in order to gain intel or cause mischief
Building hidden guerilla bases in the mountains
Stealing cargo airplanes from Drassen airport and using them for bombing runs
Making incursions into Tracona (neighboring country)
Sabotage missions (blow up airplanes, radar dishes, command bunkers, radio towers, etc)
Psychological warfare (drop propaganda leaflets, take over national TV network, blackmail army generals, etc)
Making elaborate town defenses (barbed wire, foxholes, mines, explosives, caches, etc)
POW rescue missions
Any guns/skills/items/enemies/terrorists/whatever you want
Hearts & minds (get water/electricity/medical care/sanitation/food established, not enough to just train militia)
More exotic missions (off the top of my head: guard convoy against bandits, parachute into besieged base to relieve defenders, stage an urban coup in Meduna, perform a heist against the national bank, flush out tunnel rats from underground bunkers, protect VIPs from assassins, help Hans make a porno to fund the resistance, go abroad to recruit mercs, kidnap scientists and make them work for you, steal the Chalice in a stealthy way, set up a wildlife sanctuary for all the bloodcats, send flowers with anthrax to Deidranna)

I'd vote for the Twilight2000 rules. It has all the guns allready. Or better yet the Traveller TNE version of the same GDW House rules system.

If I could mod JA2 I'd turn it into a combined Striker/Cadre mission as described in the Traveller supplement Striker. The Imperium contracts for mercinarys on a backwater Tech 8 world. You could then bring in some higher tech slug throwers like 7mm and 9mm ACR's and 4mm Gauss rifles etc.

I just felt like adding D&D has 'funny-dice', other than 6-sided, I used to be so impressed by those things.
But with several normal dice you could do numbers above 6 as well. (could even roll 1 dice multiple times adding the outcomes.)

Stats/skills affect the outcome of actions.
The jagged-ingame-help contains info on stats-and-the-actions-they-affect (h-key while on the laptop-websites-screen)

I'm at a loss about calculating,
.. an X-percentage outcome means X-times_out_of_a_hundred, I want to know of one-instant.
.. and 0.something just reeks of percentage ...

I would use the Basic Roleplaying (BRP) system by Chaosium. Its most famously used in Call of Chutluhu (CoC)roleplaying game, but is not limited to that game. I used it to play a tactical assault on a warlord in Cote d'Ivor with three players trekking through the countryside in a very JA like manner.

The game system is easy, just roll a d100 and check against your sheet if you made a success.

Me and some friends are gonna run through the JA setting as a pen & paper campaign, possibly also with some miniature wargaming for major battles. I would like your input on all this! What game system(s) to use? How to translate merc stats? Any other suggestions? How would you do something like this? What possibilites would porting JA to the pen & paper format bring with it?

Twilight 2000 would probably be the most natural system. You could always use the d10-based version and tweak it to percentile for Jagged Alliance-style stats. The BRP system used in Call of Cthulhu would be the easiest fit since it's percentile based (as Arquebus mentioned), but Twilight 2000 would pretty much be ready made for tons of guns. Plus, you've got tanks and hummers and all the weapons of mass destruction you could possibly want. Hit locations and such, too. I've always been a fan of Twilight 2000 for modern day, realistic campaigns.

Personally, I've played in JA2 themed games where the GM used GURPS by Steve Jackson Games, and it worked very well. I've also used it to play TW2000 themed games, for that matter. For either, I'd recommend the supplement 'GURPS High Tech', as it has a rather extensive selection of specific modern firearms (while the core book just has generic weapons like 'Tech Level 7 5.56x45mm Assault Rifle').

SJG offers GURPS Lite for free download as a .pdf on their website. It's a compressed 'starter pack' of the rule system.

I never really cared much for GURPS, personally. Not that I hate it, by any means. I like the amount of character tweaking you can do, but as a jack of all trades system, it's naturally a master of none. I have yet to encounter anything GURPS can do that isn't done better in some other system that focuses specifically on a genre.

That said, it's not a bad system, and its versatility makes it an interesting option for campaigns that mess with time or dimensions, so you can bounce people through all manner of craziness with one set of functional rules. I would rather run a Rifts campaign using GURPS than actually using Rifts. Granted, I hate the Palladium system.

The system mechanics for Shadowrun suck ass in a big, big way. I still run it on occasion just because there's so much shit you can throw at people, but I absolutely loathe the nuts and bolts of the system.

Granted, it does have a certain bootstrapped possible mortality to almost anything, if someone gets lucky enough. Twilight 2000 does it way better, though.

AmnesiaLab: Mmmph. Palladium. Yeah. If one wanted to run a JA2-type game and have it make as little sense as possible, one could always dig up their old Recon/Revised Recon RPG. When in came to GURPS, I never really picked up the whole 'master of none' thing. The old adage is that one can never say there isn't a rule to cover a particular situation in GURPS, only that one hasn't found the fine print for it yet. It is in its basic concepts rather simple, but gets notably focussed as needed.

But yeah. Still, for modern shoot 'em up that bore a passing resemblance to reality, with actual squad-level tactical combat... TW2000 was something of a gem, particularly considering that it's from a time when the bar wasn't exactly set very high for RPG's.

In no cases would I use D20 Modern - too abstract and too weird rules-wise, and full of Murphy's which would become glaringly obvious in a JA2-themed game, such as:
*a bullet-proof vest being more likely to stop a round from a Ma Deuce than a Glock.
*body armor increasing your risk of taking damage from grenades and sprayed auto-weapons fire rather than reducing it.

A longer review is not available at the moment, because the millenniumsend-site is still down (it had been hacked...).

Found the review:

Millennium's End (ME) calls itself a "Roleplaying Game in the Techno-Thriller-Genre", which is essentially true. It is set in the near future, which was meant to be 10 years in the future, but as the books were published at the beginning of the 90s, this background as already been overtaken by the presence. But this seems to be the only bad thing about the game, and it is not that bad, because you do not have to throw away ME's history and learn a new one, you already know the history: It is ours.
Player Characters in ME are meant to belong to "BlackEagle/BlackEagle Security and Investigations", a company that acts worldwide and has offices in the most important cities of the world. These offices act as liaison between the customer and the operations teams (called 'cells'). Even with the changed history there is an abundance of jobs for a BlackEagle cell, be it special operations, espionage and counterespionage, surveillance, investigations, body guard duty or green terrorism. The locations for this can stretch from the jungles of South America to the penthouses of the rich in Las Vegas. And all of this can be done on both sides of the law (though carefully).
Another reason for ME's sophistication is the fact that adventure ideas can be taken from everywhere, be it a Hollywood movie or a newspaper, and a simple atlas is a better world description than the sourcebooks you find for other games.
When I myself referee a game of Millennium's End, my players portrait a group of white-collar gangsters in the USA of 2002. Their jobs range from stealing masterpieces of art from wellguarded museums to stopping transports of chemicals (with the use of heavy firepower) in order to make a profit in the stock market. The setting is our time, the here and now. And movies like "Mission Impossible", "Sneakers" or "Hudson Hawk" give me adventure ideas.
And that is a big plus for ME: the real world is its setting, and we know this world better than any other world. Nowhere else can we count on things to happen as they should do, from our experience, so improvisation is much easier and common sense works well here, where no gods or sorcerors change the physics of the world.
Millennium’s End has a good deal of realism, more so than any other roleplaying game I encountered so far.
As mentioned earlier with the example of my own group, player characters in ME can be other people than BlackEagle operatives, they can be police or military, or any other people who work in teams.

The rules are working on a D100- or percent-system, which is somewhat similar to that of Call of Cthulhu. Character creation takes some time: 10 attributes are weighted first, rolled up and added to a base value dependent on the sex of the character. These attributes are then used to derive values for different talents, which are the base for skills. Furthermore, the attributes are a base for some secondary attributes. One of the attributes gives the player the skill points with which to buy the character's skills.
If the player has a concept for his character, he can simply choose those skills that he think will fit the character-concept. If he has no concept, he can choose the skills he wants for his character and then think of a way how his character acquired these skills. This is easily facilitated by the use of 'skill packages', groups of skills that are usually taught together for some reason or another (for example, the "BlackEagle Entry Training Course"). Additionally, there are some 'bottom line'-skills that any character in a modern campaign should have (for example "Swim").
Having done this (after 2 to 3 hours), the character is almost ready, and one does not have to re-calculate the character's values too often. The characters are normal people, you will not get supermen. Using the values, once calculated, is quite easy. And adding skills that are not covered yet is quite easy as well.
There are no abstractions like hit points. If a character is wounded, the wound will make using skills difficult, and if a wound is bleeding, it will make his life quite short if no medical help is administered.
Due to the percent-system of skill-use, there is a chance for the player to see his chances of success, but this will be a rather basic chance, as the situation may make modifiers needed to apply to the skill-roll. For the reason of modifiers, skills may reach values above 100%, and there is an additional system to rank skills to see whether the character is familiar with a skill, competent in it, or if he is already an expert.
Equipment is a very important thing for characters in ME. ME has the biggest equipment source of all: the world. There are lots of things useful, but do you need to carry all of them with you on each and every job?
There are rules for computer-hacking, but these are somewhat abstract and could use a little bit of spit and polish.
The combat-system is quite realistic. Your target is represented by a silhouette broken up into different areas that react differently to being wounded. On this target a transparent overlay is placed that has a point of aim in the middle, with other points around the middle that constitute near misses. There are different overlays for different ranges, which include modifiers to the to-hit roll. If your roll is not enough to hit your point-of-aim, it may be near enough to hit another location on the target, or some innocent bystander.You will not need modifers for cover, though, just put a slip of paper over that part of the target that cannot be seen. If your roll lands on a 'near miss' on the cover, the target is not hit (if the cover is sturdy enough). And unlike other games, where you can easily shoot the gangster without thinking about the hostage, in ME you will see that quite a lot of the 'near miss'-points are on the hostage, and you may think twice whether to take your chances.
There are no critical hits in this system, the best you can achieve is to hit what you aimed for. And there are no critical failures either, the worst you can get is a miss that hits something valuable. If you want, you can introduce a weapon failure for very bad rolls, though.
A torso or head hit on an unarmored target is quite fatal under this system (which needs some calculation, but you can find some precalculated tables on the internet, made by the ME-community, to speed up the process). Even if not instantly fatal, wounds can make life very difficult for the target, so even nonfatal hits can produce casualties.
So do not hang on to your characters too much, or make them wear personal ballistic armor. Damage in ranged combat is dependent on the bullet, not on the weapon which fires the bullet, so damage values are tied to the calibre and type of bullet used. Oooh, by the way, even people count as armor for those people standing behind them, so choose your ammo wisely, or you may kill someone inadvertently.

Millennium’s End was produced at the beginning of the 90s of the last century by a company named Chameleon Eclectic Entertainment, the license today lies with Hero Games and is not used. The material produced was in English only. As ME is out of print for some time now, your chances to lay your hands on a copy are slim, you will have to scour the internet for it (post some 'want'-ads) or have a look at ebay.
In short: Millennium’s End is a lot better than Shadowrun, because of the realism (no cyberware, no meta-humans, no magic; therefore no powergamers and munchkins). It's sophistication puts it above Cyberpunk (no character classes) and GURPS:SpecialOps (more flexibility). The background needs some work, though, but sources come up daily or weekly (newspapers and journals), or you may simply add 10 years to the published timeline. With a little work, you'll get the best of Techno-Thriller-games!

ME-products, according to my knowledge, are:
Millennium’s End – core rules: enough to start your game. Just ad some info from the internet and you are ready to go.
Game Master’s Compendium: the best of its kind, not just for ME, but for all contemporary or near future games.
Gamemaster Screen: not really useful, considering the '1999 data source' that comes with it is outdated by far. But it's funny to read.
Ultra Modern Firearms: Guns that were modern at the beginning of the 90s, but most of them are still in use today. The pencil-drawings are better than photographs, and the book contains mostly real life data and descriptions. ME-specific data is concentrated in a few tables at the end of the book. And there is a table in front that lets you choose the right gun for your purpose, without knowing brand or model first.
Vehicle Sourcebook: descriptions for some cars, bikes, boats, helicopters, hovercrafts, planes and the like. Due to the variety of vehicles, there are only a few examples per class, but an emphasis has been made to get examples of both civilian and military vehicles. ME-specific rules are at the end of the book, as with Ultra Modern Firarms.
Miami Sourcebook : Outdated and somewhat fictional data about Miami, but great NPCs and a description of the Miami office of BlackEagle.
Medellin Agent: a sourcebook with an adventure at the end. It covers a fictional war between FARC and the drug cartels on one side and the Colombian government with its US-based help on the other. Plenty of work for a BlackEagle cell, or any other covert action team. Covers daily life in Colombia and the military campaign mentioned before.
Terror/Counterterror: well researched sourcebook that differentiates between the different terrorist organizations as to reason, funding, public acceptance, etc. Gives data on what BlackEagle knows and what is really going on. The terrorist and counterterrorist organizations are sometimes real world and sometimes fictional.
Nightwalker/The Villee Affair: three adventures for a team of player characters

Thomas Echelmeyer, translation from German to English by Martin Volkmann

AmnesiaLab: Mmmph. Palladium. Yeah. If one wanted to run a JA2-type game and have it make as little sense as possible, one could always dig up their old Recon/Revised Recon RPG. When in came to GURPS, I never really picked up the whole 'master of none' thing. The old adage is that one can never say there isn't a rule to cover a particular situation in GURPS, only that one hasn't found the fine print for it yet. It is in its basic concepts rather simple, but gets notably focussed as needed.

But yeah. Still, for modern shoot 'em up that bore a passing resemblance to reality, with actual squad-level tactical combat... TW2000 was something of a gem, particularly considering that it's from a time when the bar wasn't exactly set very high for RPG's.

In no cases would I use D20 Modern - too abstract and too weird rules-wise, and full of Murphy's which would become glaringly obvious in a JA2-themed game, such as:
*a bullet-proof vest being more likely to stop a round from a Ma Deuce than a Glock.
*body armor increasing your risk of taking damage from grenades and sprayed auto-weapons fire rather than reducing it.

Yeah, it's no offense to GURPS. It's just hard to top Twilight 2000 for realistic modern combat. And yeah, D20? Ouch. I hate, hate, HATE the d20 system, and I hate the fact that they basically made it open source so anyone can use it. It's fucking awful. Ever played d20 Star Wars? Dear God. Talk about shoehorning a game into a system that doesn't work for it. I wasn't wild about the original West End Games version of Star Wars, but the system mechanics worked for the game. A tweaked version of the old one would have been way better.

In general, I dislike level-based systems. Skill-based systems are the way to go for any game that wants to have any semblance of realism. Level-based systems turn into complete hack and slash.

And to Starwalker--

That system sounds pretty awesome for combat. I might have to see if I can get my hands on it. Thanks for the suggestion.

No disrespect construed at all. TW2000 was (and remains) an awesome system. Millennium's End is also a lot of fun (though I personally have a tendency to shun systems in which generating characters involves rolling dice and/or rip off their settings to run in GURPS). I'm not sure I agree with the point about it being more versatile than GURPS (versatility being its key strong point), and all of the situations that he described with hostage situations, shooting through targets, shooting through cover, etc aren't really unique to ME (GURPS rules for all of those situations start running through my head), but it is good fun to play and generally produces sane results.

And oh yes, I've tried D20 Star Wars myself too. I'll give it this - it's pretty, and better organized than those old WEG D6 Star Wars books that look like they were produced in someone's garage. Now if only it had a real system under the hood!

Level-based systems always struck me as being about bragging rights, in the "I'm a level 20 so and so," sort of way. Apart from that, it's hard to discern where it becomes a perk at all. It works (in a fashion) for epic fantasy where you have a few characters who are metaphorical giants who stand above the rest of humanity (or dwarfdom, or whatever) and everyone else is hapless little scrubs. It doesn't play well for gritty games where heroes are mortal men.

Yeah. It works just fine for the stand hackfest "We're off to kill the dragon!" kind of games (which I'll play on rare occasions, but I just don't generally care for) but absolutely worthless for anything else. It's hard to have a good story in a game like that because everyone wants to go kill shit to get experience. Half the time I run a modern game, there might be one instance of combat in a four or five hour session. With a skill-based game, character development isn't based on combat, so you can really let a story breathe.

I'm not saying I'm always light on combat, but I don't like being forced to provide combat just for the sake of rolling dice and getting XP, and that's just what generally happens in level-based systems.

If you are going pen and paper, I always liked the model approach used in some of the Games Workshop spin-off's that were in my opinion better than the main games because they had more RPG in them.

The two systems I am specifically referring to are Warhammer Quest and Necromunda. Parts of WHQuest that were great for RPG's were the in town parts which added a lot to the characters I think (though a lot of my friends found it took more time in town than it did in dungeons). Thought the system that will suit JA2 would more than likely be the Necromunda one which is totally focused on squad combat. There is a level system in place but that can easily be removed to just activate skils.

GURPS would be perfect for JA2 as it actually is tuned for "realistic" RPGing. By realistic I mean normal/real people. It has some trouble with high powered superheros, anime, and stuff like that. I use it for doing XCom (aka UFO) and Fallout at conventions and it works perfectly.

Also, a lot of gearheads use GURPS so the gun rules and such are pretty accurate given RPG abstractions. They remind me of a lot of you guys.

As for d20 (3/3.5) it works fine for one kind of RPG, the silly over-the-top Conanesque kind, and is particularly poor at handling "realistic" stuff. I played a Traveller T20 event at a convention and the combat was utterly ridiculous. Their attempts to make gun combat deadly particularly flopped IMO.